Variant calling isn't run when using --skip_asciigenome with metagenomic data

[svarona]

Description of the bug

When I run the pipeline with the param --skip_asciigenome, variant calling steps won't be performed.

Command used and terminal output

# Command used:
nextflow run /scratch/bi/pipelines/nf-core-viralrecon-2.4.1/workflow/main.nf \
          -c ../../DOC/viralrecon_metagenomic.config \
          --input samplesheet_MW536483.1.csv \
          --outdir MW536483.1_20220712_viralrecon \
          --platform illumina \
          --protocol metagenomic \
          --variant_caller ivar \
          --consensus_caller bcftools \
          --fasta /data/bi/references/virus/herpesviridae/MW536483.1.fasta \
          --gff /data/bi/references/virus/herpesviridae/MW536483.1.gff \
          --kraken2_db "/data/bi/references/eukaria/homo_sapiens/hg38/UCSC/kraken2/kraken2_human.tar.gz" \
          --skip_pangolin \
          --skip_nextclade \
          --skip_plasmidid \
          --skip_asciigenome \
          --min_mapped_reads 500 \
          -resume

# Terminal Output seems to be fine:
-[nf-core/viralrecon] 3/10 samples passed Bowtie2 500 mapped read threshold:
    4378: DTA2
    939: DTA5
    555: H62
-
-[nf-core/viralrecon] 7 samples skipped since they failed Bowtie2 500 mapped read threshold:
    20: DTA1
    231: DTA3
    277: DTA4
    27: H61
    36: H64
    50: H63
    186: H65
-
-[nf-core/viralrecon] Pipeline completed successfully-
Completed at: 12-Jul-2022 17:11:31
Duration    : 56m 21s
CPU hours   : 13.9
Succeeded   : 182


# Folder content misses ivar:
$ ls MW536483.1_20220712_viralrecon/variants/

bowtie2

Relevant files

Custom config file: viralrecon_metagenomic.config

singularity {
	enabled = true
	autoMounts = true
}

process {
	executor = 'slurm'
	queue = 'middle_idx'
	withName: 'FASTP' {
            ext.args = '--cut_front --cut_tail --trim_poly_x --cut_mean_quality 20 --qualified_quality_phred 20 --unqualified_percent_limit 10 --length_required 50'
        }
}

params {
	max_memory = 376.GB
	max_cpus = 32
	max_time = '48.h'
}

.nextflow.log file

nextflow.log

System information

• Nextflow version 21.10.6
• Hardware HPC
• Executor Slurm
• Container engine and version: Singularity v3.7.1
• OS and version: CentOS 8

[svarona]

Issue update with test dataset:

Description of the bug

When I run the pipeline with the param --skip_asciigenome in metagenomic mode with ivar variant caller, variant calling steps won't be performed.

Command used and terminal output

# Command used:
nextflow run /scratch/bi/pipelines/nf-core-viralrecon-2.4.1/workflow/main.nf \
          -c ./viralrecon_metagenomic.config \
          -profile test_sispa \
          --outdir test_viralrecon_tris \
          --variant_caller ivar \
          --skip_asciigenome

# Terminal Output seems to be fine:
-[nf-core/viralrecon] 3/4 samples passed Bowtie2 1000 mapped read threshold:
    14392: SRR11140746
    19990: SRR11140744
    16894: SRR11140748
-
-[nf-core/viralrecon] 1 samples skipped since they failed Bowtie2 1000 mapped read threshold:
    738: SRR11140750
-
-[nf-core/viralrecon] Pipeline completed successfully-
Completed at: 12-Jul-2022 19:20:26
Duration    : 3m 30s
CPU hours   : 1.5
Succeeded   : 133

# Folder content misses ivar:
$ ls test_viralrecon_tris/variants/
bowtie2

Relevant files

Custom config file: viralrecon_metagenomic.config

singularity {
	enabled = true
	autoMounts = true
}

process {
	executor = 'slurm'
	queue = 'middle_idx'
}
params {
	max_memory = 376.GB
	max_cpus = 32
	max_time = '48.h'
}

System information

• Nextflow version 21.10.6
• Hardware HPC
• Executor Slurm
• Container engine and version: Singularity v3.7.1
• OS and version: CentOS 8

[saramonzon]

We've just detected that with this fix it breaks again the issue #286 when --skip-asciigenome or protocol=metagenomic

We think the process CUSTOM_GETCHROMSIZES can be run always, not only when the protocol is amplicon or the asciigenome process is run, what do you think @drpatelh, if you agree we can prepare a small PR with some minor bug fixes on the ivar_variants_to_vcf script we've already detected and fixed.

[drpatelh]

CUSTOM_GETCHROMSIZES will always be run now as added in f7f99f7